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Structural basis for substrate selection by the SARS-CoV-2 replicase.

Brandon F Malone1, Jason K Perry2, Paul Dominic B Olinares3

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|February 1, 2023
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Summary
This summary is machine-generated.

Structural insights into the SARS-CoV-2 replication-transcription complex (RTC) reveal how it distinguishes natural nucleotides and incorporates antiviral remdesivir triphosphate (RDV-TP). This guides the design of novel antiviral therapies.

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Area of Science:

  • Structural biology
  • Virology
  • Drug discovery

Background:

  • The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) forms the replication-transcription complex (RTC), a key target for antiviral drugs like remdesivir.
  • Understanding how the RTC selects nucleotide triphosphates (NTPs) for viral RNA synthesis and how antivirals compete is crucial for developing effective inhibitors.

Purpose of the Study:

  • To elucidate the structural mechanisms by which the SARS-CoV-2 RTC recognizes natural NTPs and incorporates antiviral nucleoside analogues.
  • To provide a structural basis for the selective incorporation of remdesivir triphosphate (RDV-TP) over adenosine triphosphate (ATP).

Main Methods:

  • Cryogenic-electron microscopy (cryo-EM) was employed to visualize the RTC in complex with natural NTPs and RDV-TP.
  • Structural analysis focused on the interactions governing nucleotide binding and incorporation.

Main Results:

  • Detailed structures of the RTC bound to natural NTPs in pre-incorporation states were obtained.
  • The structural basis for the selective incorporation of RDV-TP, differentiating it from ATP, was revealed.
  • Nucleotide recognition by the nsp12 NiRAN domain, including selective binding of guanosine triphosphate (GTP), was characterized.

Conclusions:

  • The findings explain the molecular interactions essential for NTP recognition by the RTC, informing the rational design of novel antiviral agents.
  • Insights into NiRAN domain function support its role in 5' RNA cap formation, crucial for viral propagation.